The one advantage you would be missing out on is the ability to use up to 8 IDE devices in your system! If you have three hard drives, a CD-ROM drive, and a CD-RW drive, this may be very appealing to you. Along similar lines, four independent IDE channels (two on the motherboard and two on the HotRod66) would allow you to configure all your IDE devices as master.
Separating your devices in this manner would improve disk access since any of thefour IDE channels could be accessed at the same time. In a master/slave configuration, only one device can be accessed at a time.." NULL